--- layout: archive title: Zulip Chat Archive permalink: /stream/113488-general/topic/Universe.20issues.html ---
I seem to not understand universes properly, or more precisely how to use them properly. I ran into the following issue with some code:
definition foo (X : Type*) := ∀ (β : Type*), true theorem baz (X : Type*) (bar: foo X) (β : Type*) : true := begin have H := bar β, -- error admit, end
The error was
type mismatch at application bar β term β has type Type u_3 : Type (u_3+1) but is expected to have type Type u_2 : Type (u_2+1) state: X : Type u_1, bar : foo X, β : Type u_3 ⊢ true
I figured I'd investigate more, so I next wrote this:
universes u v w x set_option pp.universes true definition foo' (X : Type u) := ∀ (β : Type v), true theorem baz' (X : Type w) (bar' : foo' X) (β : Type x) : true := begin have H := bar' β, -- error admit, end
and this time I got
type mismatch at application bar' β term β has type Type x : Type (x+1) but is expected to have type Type u_1 : Type (u_1+1) state: X : Type w, bar' : foo'.{w u_1} X, β : Type x ⊢ true
This made me realise that I didn't understand what was going on, because there is still this universe u_1
mentioned, even though I thought I'd just explicitly written down what universe everything was in.
In particular, bar'
seems to mention this universe u_1
and I'm not sure where this universe got involved.
Some experimentation led me to something which worked:
definition foo'' (X : Type u) := ∀ (β : Type u), true theorem baz'' (X : Type v) (bar'' : foo'' X) (β : Type v) : true := begin have H := bar'' β, -- works exact H end
i.e. "keep X and beta in the same universe and you'll be fine"
But this raises two questions for me:
1) why wasn't I fine before?
2) Will this fix cause me problems later?
In reality, X is a topological space and it is covered by open sets U i
where each i
has type beta
that is, U : beta -> set X
My instinct is always to just let everything live in different universes because who cares about universes anyway, that's the joy of type theory
In ZFC I would just let X and beta be in Type
but that might be a bridge too far
When you defined foo
, it had two universe parameters, corresponding to the two Type*
instances
what does that even mean
foo is a thing
and it has a type
which lives in a universe
it is universe polymorphic
Think of it as being implicitly a forall over the universe variables
except that lean has no universe variable binders, so it's all just free variables and substitution
foo'
mentions a universe I don't even see
or at least something mentions this universe
foo
and foo'
are the same
wait
are they exactly the same?
except foo'
is more explicit about the two universe variables, u
and v
Should I think that foo'
is really "for all universes u, ..."
yes, they are exactly the same as far as lean is concerned
yes. All universe polymorphic functions are like this
like when I make variables and then secretly I am writing "for all v..."
exactly
But where is this u_1
coming from?
Didn't I name all my universes with foo'
?
foo'
has two universe variables, named u
and v
in the definition, but since it's like a forall, whenever you use it these variables can be substituted for other things
gotcha
So foo'
is for all universes u and v, [what I wrote]
so why do I get a problem?
why can't we just do universe unification or something?
u_1
is the name of a universe variable in baz'
, since you reference foo' X
which only fixes its first parameter by unification, lean invents a second variable u_1
so it becomes bar' : foo'.{w u_1} X
aah
yes I just independently realised this
But now bar'
should be "for all universes u_1, ..."
it is
bar'.{w x u_1}
has type forall (X : Type w) (bar' : foo'.{w u_1} X) (β : Type x), true
And since u_1
and x
are separate universe variables being generalized, inside the proof you can't assume they are equal
so bar' β
is a type error since bar'
accepts a Type u_1
OK so you have convinced me that the underlying way that universes work mean that my initial attempts should not work.
So now the question is should I try to re-arrange things to make them work?
just write foo'.{w x}
instead of foo'
in the type of bar'
Or should I go down the "might bite me later and I have no understanding as to whether it will" route of letting all universes be u
aah, oh great, so I can do what I want to do.
In general, I try to avoid types with "internal universe variables" like foo'
here, which has a forall whose universe is not constrained by the input parameters
definition foo' (X : Type u) := ∀ (β : Type v), true theorem baz' (X : Type w) (β : Type x) (bar' : foo'.{w x} X) : true := begin have H := bar' β, -- works :-) exact H, end
I need to think about the last thing you said
that means to prefer def foo' (X : Type u) := ∀ (β : Type u), true
over def foo' (X : Type u) := ∀ (β : Type v), true
because this is a massively minimised thing and in reality I will have to decide whether I can try to avoid the thing you want me to avoid
Thanks a lot for the fix and the advice though.
How do I know whether the thing you prefer will be safe for me?
hmm, I need to go and feed children
thanks
It is slightly less universe parametric (it requires that two variables be the same), so you may need extra ulift
s around, which may or may not be better than the often required .{w x}
stuff that arises with this approach
Generally you will have to be "universe conscious" when working with definitions with internal universe variables - lots of things will require annotation. cardinal
, ordinal
, and Set
(the ZFC sets) are like this
category
may also be, this exact thing was a point of discussion with Scott a few weeks ago
What is happening here:
universe u structure scheme := (β : Type u) theorem scheme_of_affine_scheme (R : Type u) : scheme := { β := R -- universe issue } /- type mismatch at field 'β' R has type Type u : Type (u+1) but is expected to have type Type u_1 : Type (u_1+1) -/
Seems to me that scheme has decided that it wants to live in a different universe to beta and R
oh
heh
ignore the irrelevant names
If I change theorem to definition, it works
And this works too:
theorem scheme_of_affine_scheme (R : Type u) : scheme.{u} := { β := R -- works }
OK so maybe the answer is simply "don't use theorem to define something which isn't a Prop"
definition scheme_of_affine_scheme (R : Type u) : scheme := { β := R -- works }
I guess I don't understand what's going on, but on the other hand I can see I was doing something dumb.
This gives some small insight.
set_option pp.universes true def scheme_of_affine_scheme (R : Type u) : scheme := begin -- R : Type u -- ⊢ scheme.{?l_1} end lemma scheme_of_affine_scheme (R : Type u) : scheme := begin -- R : Type u -- ⊢ scheme.{u_1} end
Aah so in the first case scheme is in some universe and Lean isn't too fussed, it will decide later
but in the second case Lean decided to go for it and make a decision
because it's a lemma so the universe is supposed to be Prop
and it wasn't Prop so Lean panicked
The lemma card_univ
below does not work without the .{u}
in the fintype
instance
import data.set.finite open set fintype universe u def equiv_univ (α : Type u) : α ≃ (set.univ : set α) := { to_fun := λ a, ⟨a, mem_univ _⟩, inv_fun := λ a, a.1, left_inv := λ a, rfl, right_inv := λ ⟨a, ha⟩, rfl } @[simp] lemma card_univ {α : Type u} [fintype α] [fintype.{u} (set.univ : set α)]: @fintype.card (set.univ : set α) _ = fintype.card α := eq.symm (@card_congr α (set.univ : set α) _ _ (equiv_univ α))
The following do not work.
set_option pp.universes true @[simp] lemma card_univ {α : Type u} [fintype α] [fintype (set.univ : set α)]: fintype.card (set.univ : set α) = fintype.card α := eq.symm (card_congr (equiv_univ α))
Gives the error
failed to synthesize type class instance for α : Type u, _inst_1 : fintype.{u} α, _inst_2 : fintype.{?l_1} ↥univ.{u} ⊢ fintype.{u} ↥univ.{u}
and
set_option pp.universes true @[simp] lemma card_univ {α : Type u} [fintype α] [f : fintype (set.univ : set α)]: @fintype.card (set.univ : set α) f = fintype.card α := eq.symm (@card_congr α (set.univ : set α) _ f (equiv_univ α))
Gives the error
type mismatch at application card_congr.{u u_1} (equiv_univ.{u} α) term equiv_univ.{u} α has type equiv.{u+1 (max 1 (u+1))} α (@coe_sort.{(max (u+1) 1) (max 1 (u+1))+1} (set.{u} α) (@set.has_coe_to_sort.{u} α) (@set.univ.{u} α)) : Type u but is expected to have type equiv.{u+1 u_1+1} α (@coe_sort.{(max (u+1) 1) (max 1 (u+1))+1} (set.{u} α) (@set.has_coe_to_sort.{u} α) (@set.univ.{u} α)) : Type (max (max u u_1) u_1 u)
What's going on here? And will the .{u}
in the fintype instance make the lemma more difficult to use. It worked in my application, but will it always work?
And will the .{u} in the fintype instance make the lemma more difficult to use.
No, not at all. It is the only possible choice, the elaborator just can't figure it out for whatever reason.
(The universe parameter .{u}
is always there, whether you write it explicitly or not.)
Last updated: Apr 24 2020 at 19:02 UTC


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"Rush Hour 2" - Feels Kinda Slow by Homer Yen (c) 2001
What has fueled the excitement around "RH2"? Arguably, the team of Chris Tucker and Jackie Chan is the best cop/buddy combo since those guys from "Lethal Weapon." Summer moviegoers are looking for a fun time, which is almost guaranteed when you watch either of these two flamboyant stars. And, the first "RH" was so much fun that you can't help but have high expectations for this one.
With expectations as high as a mountain, it's almost impossible for a movie to overcome this kind of barrier. And this one can't, falling short on laughs and defining moments. In fact, many will think that the most memorable moments were the outtakes at the film's end and the cameo by actor Don Cheadle who speaks Cantonese and displays the Tiger Claw fighting style.
But the film is not all bad thanks to Chris Tucker, who as Detective James Carter, is the life of the party. In the film's first act, he's in Hong Kong visiting his old pal, Inspector Lee (Chan). However, Lee is always on the job and is currently trying to solve a recent bombing, suspected to have been carried out by Ricky Tan (John Lone), a notorious Triad gang leader.
Carter just wants to have a good time, and when he whoops it up at a Karaoke bar, Lee begs him to remain incognito for this is where Triad gang members tend to hang out.  "I'm from LA; we invented gangs," he says. Turning to the crowd, he screeches, "All the Triads and the ugly women on the left side, all the f-f-i-i-i-n-e women on the right side." Tucker's brassy demeanor, his down-with-it attitude and his cluelessness about the culture and the language make him hilarious to watch.
Unfortunately, after the first 30 minutes, our duo leaves Hong Kong and all the fun behind. The investigation leads them to Los Angeles and Las Vegas where it's Chan's turn to play the fish-out-of-water. But, he looks uncomfortable when speaking English and doesn't possess Tucker's insouciance. Chan seemed statelier and more at ease in the first "RH." His role was more dramatic in nature, and he didn't have to speak too much English. This film lightheartedly acknowledges Chan's broken English when he asks, "don't you understand the words that are coming out of my mouth?" Tucker replies disgustedly, "don't nobody understand the words coming out your mouth!" Even the outtakes show many scenes where Chan is trying to force his English lines.
Also missing are the great stuntwork and fight sequences that are hallmarks of Chan's work. The only good sequence occurs early on where Chan goes against a cadre of gangsters atop rickety scaffolding several stories above. But the other sequences seemed tepid or looked cartoonish.
"RH2" is only marginally fun to watch while short on drama. Yet, it received so much press and hype that it succeeded in grossing over $69 million in its opening weekend. This is an incredible accomplishment! And considering the fact that August is the slowest of summer movie months (the previous opening record in August was "Sixth Sense" which took in about $27 mil.), moviegoers couldn't wait to see Jackie Chan and Chris Tucker reunite. But what's the hurry? "RH2" felt kinda slow.
Grade: B-
S: 1 out of 3 L: 1 out of 3 V: 1 out of 3
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{{Infobox prepared food | name = Mafaldine | image = | caption = | alternate_name = Reginette | country = Italy | region = | creator = | course = | type = Pasta | served = | main_ingredient = | variations = | calories = | other = }} {{Refimprove|date=June 2008}} Mafaldine, also known as Reginette (Italian for little queens) or simply Mafalda, is a type of ribbon-shaped pasta. It is flat and wide, usually about 1 cm (½ inch) in width, with wavy edges on both sides. It is prepared similarly to other ribbon-based pasta such as linguine and fettuccine. It is usually served with a more delicate sauce.
Mafaldine were named in honor of Princess Mafalda of Savoy (thus the alternative name "little queens").<ref>{{cite web|url=http://italianfood.about.com/od/pastabasics/ig/The-Pasta-Shapes-Gallery/Reginette--long-strips.htm|title=Reginette|last=Phillips|first=Kyle|publisher=about.com|accessdate=2009-07-03}}</ref>
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Ability
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Each Ability is tied to a specific Element. This Element is used to determine which of the Character’s EMs are raised and lowered and which EM Die the Enemy uses to defend against the Ability Die.
Rank
Rank determines the Elemental strength of the Ability. The Rank is used to determine how much the Character’s EMs are raised and lowered as well as track how attuned the Character is to a specific Element. At Level 1, the Character is able to purchase any Rank 1 Ability. However to purchase higher Rank Abilities, the Character must have purchased at least one Ability that is one Rank lower of the same Element.
CP Cost
CP Cost is how much CP the Character needs to spend in order to purchase an Ability.
Type
Type categorizes Abilities in Damage, Control, Support or Passive based on the Ability’s Effect.
- Damage: Deals Element Damage to an Enemy.
- Control: Places Penalties or harmful Conditions on an Enemy.
- Support: Heals or gives helpful Condition to an Ally.
- Passive: Grants the Character Bonuses or unique Effects to themselves.
AP Cost
AP Cost is how much AP the Character needs to spend on their Turn to use the Ability in Combat.
Cooldown
Cooldown is the number of Turns the Character must wait before using an Ability again. Cooldowns are reduced by -1 Turn at the End of the Character’s Turn.
Die Roll
Die Roll indicates the specific Attacker Roll used for the Ability.
Target
Target indicates if the Ability affects Allies, Enemies, the Character or an AoE.
- Ally: The Ability affects the Character and/or the Character’s Ally.
- Enemy: The Ability affects the Character’s Enemy.
- Self: The Ability affects only the Character.
- Target: The Ability can affect Allies, Enemies or Self.
- AoE: The Ability affects multiple Targets in an area. (See Combat for more)
Range
Range indicates the maximum number of spaces away from the Character the Target can be. For AoEs, Range indicates the number of spaces away from the Character the Ability begins or the maximum number of spaces away the AoE reaches. (See Combat for more)
Effect
Effect is what the Ability does when used in Combat. Abilities have a variety of Effects that are useful in a variety of situations.
Special
Special is either an additional or upgraded Ability Effect that is used if the Character meets the indicated requirements listed.


Interface that aggregates a Zend\Paginator\Adapter\Abstract just like IteratorAggregate does for Iterators.
Plugin manager implementation for paginator adapters.
Enforces that adapters retrieved are instances of Adapter\AdapterInterface. Additionally, it registers a number of default adapters available.
Class allowing for the continuous iteration of a Zend\Paginator\Paginator instance.
Useful for representing remote paginated data sources as a single Iterator
A scrolling style that returns every page in the collection.
Useful when it is necessary to make every page available at once--for example, when using a drop-down menu pagination control.
A Google-like scrolling style. Incrementally expands the range to about twice the given page range, then behaves like a slider. See the example link.


Just So Stories
by Rudyard Kipling
Just So Stories are considered some of Kipling's best works. They give fantastical explanations for various phenomena.
Source: Kipling, Rudyard. Just So Stories.
- "The Beginning of the Armadillos"
- Tortoise and Painted Jaguar come across a new kind of creature in the woods and try to decide what it is with the help of Mother Jaguar.
- "The Butterfly that Stamped"
- The story involves King Solomon, a butterfly and their wives and the question of keeping up appearences in front of one’s spouse.
- "The Cat that Walked by Himself"
- A story about the animals in the Wet Wild Woods and how the cat that walked helped domesticate all the wild animals.
- "The Crab that Played with the Sea"
- The Eldest Magician helps the Man with the flooding problem caused by Pau Amma, the monster crab.
- "The Sing-Song of Old Man Kangaroo"
- Why the kangaroo is very fast on land.
- "The Elephant's Child"
- How elephants got trunks, and how the Elephant’s Child learned to like his new feature.

- "How the Camel Got His Hump"
- A camel refuses to work and only says “humph” in response to requests for work...so a Dijnn gives him a “humph” as punishment for laziness.
- "How the First Letter Was Written"
- A drawing leads to misunderstanding then friendship.
- "How the Alphabet Was Made"
- Neolithic man Tegumai Bopsulai is out fishing with his daughter Taffy whose attempt to send a message in a drawing leads to complete misunderstanding. Taffy suggests a way of representing the sounds of the Tegumai language in pictograms. Together she and her father evolve a system using familiar objects and facial expressions, which when simplified become letters of the alphabet.
- "How the Leopard Got His Spots"
- How a leopard and an Ethiopian hunter changed the color of their skin to help them hunting the animals of the High Veldt.
- "How the Rhinoceros Got His Skin"
- Extreme itching wrinkles the rhino’s skin.
- Year Published: 1902
- Language: English
- Country of Origin: England
-
Readability:
- Flesch–Kincaid Level: 6.1
- Word Count: 30,268
- Genre: Fantasy
- Keywords: adversity, being different, camouflage, communication, discovery, growth, laziness, learning, manners, problem solving, problems and solutions, resourcefulness


{% extends "list.html" %} {% block header_title %}Authors{% endblock %} {% block results_title %}Author search results{% endblock %} {% load static %} {% load crispy_forms_tags %}
Most recent affiliation: {% include "affiliation_string.html" with department=author.main_affiliation_department institution=author.main_affiliation_institution institution_city=author.main_affiliation_institution_city institution_state=author.main_affiliation_institution_state author=main_affiliation_institution_country %}


I'm glad to let you know that we could be anyone. Anyone that loves the feeling of being alive, could be us. Anyone that feels passion for what they do, could be us. Anyone that is in love with someone else, definetly we could be them.
How you can observe this web page is not about us, this web page is about love, art, happiness... And all this little details that make the world wonderful just because of
you,
like us,
lives in it.


Stapes.js
A (really) tiny Javascript MVC microframework.
Downloads
For node.js npm install stapes
will do.
Philosophy
Right. There's a zillion other Javascript MVC frameworks, why
should i choose Stapes.js?
Here's why i think you should use it: it's really tiny (just 2kb minified and gzipped),
easy to fit in an existing codebase, and doesn't force you to
write your code in a specific style. Because of its small size it's ideal
for mobile development.
So, Stapes.js isn't a traditional MVC framework?
No. Stapes doesn't have any pre-defined Models, Views or Controllers.
It also doesn't have Collections, Routers, or stuff you might find in other
libraries (remember, it's tiny :).
Right.. so how do i write my code?
Any way you want. Stapes has all the building blocks you need when
writing a MVC app.
Like what?
Here's a list:
But what about templating, persistence, routing, history management, etc?
That's the flexibility of Stapes: you're free to use any library you want.
Right, so this is your hobby project. Does this actually work in production?
Stapes was written for a complex HTML5 media player in a high-traffic website,
and it works nicely there, as well as in multiple other projects. Have you used Stapes in your
project?
Where do i report bugs, feature requests, patches?
Please report all of those things on Github.
Does this work in all browsers?
Stapes should work on all current (mobile) browsers, as well as on
older browsers like Internet Explorer 8. If you come accross any
browser-specific bugs, please report them
on Github.
Okay, seems promising. Where do i start?
Read on...
Introduction
If you're new to writing MVC apps you probably want to read this
beginner's tutorial, and write a todo app in less than 100 lines of code using Stapes.
Write your Stapes modules like this
var Module = Stapes.subclass({
constructor : function(name) {
this.name = name;
}
sayName : function() {
console.log('My name is: ' + name);
}
});
Then, use it like this.
var module = new Module('Emmylou');
module.sayName(); // 'My name is Emmylou'
If you want to use private variables and functions, use Stapes like this
var Module = (function() {
var name;
function showPrivate() {
console.log("You shouldn't be seeing this", name);
}
var Module = Stapes.subclass({
constructor : function(aName) {
name = aName;
showPrivate();
}
});
return Module;
})();
var module = new Module('Emmylou');
However, note that this will only work with a single instance of the class because the scope stays the same. Creating an extra module will overwrite the private variables from the previous instance.
Using event methods with any non-Stapes object or function
It's possible to add the event methods to any
regular Javascript object or function. See
Stapes.mixinEvents
for more information.
Using it together with RequireJS
To avoid lots of global variables you can use a dependency loader like
Require.JS. This also makes the
previous example easier to read.
A dependency loader also makes it a lot easier to modularize your code and
(with the Require.js optimizer) easily minify and concat your app.
// 'module.js'
require(["path/to/Stapes"], function(Stapes) {
var name;
function showPrivate() {
console.log("You shouldn't be seeing this: ", name);
}
var Module = Stapes.subclass({
constructor : function(aName) {
name = aName;
showPrivate();
}
});
return Module;
});
// somewhere else
require(['module'], function(Module) {
var module = new Module('Elvis'); // You shouldn't be seeing this: Elvis
});
Examples
There are three examples available to get a taste on how to write a
Stapes.js application.
Code for these examples is available in the development download.
Note that the two todo examples are also available from
TodoMVC.
API: Creation methods
These methods aid in the creation and extension of classes, or
modules. These terms are used interchangeably in this
document.
subclass
Module.subclass( [object] )
Stapes.subclass( [object, classOnly] )
Create a new Stapes class that you can instantiate later on with
new
.
Note that until Stapes 0.6.0 the preferred way of creating new modules was by using Stapes.create
. This has been replaced by subclass
since 0.7.0. Read this blogpost why.
You can add a constructor
(the function that is run when you
instantiate the class) property to the object. All other properties
will become prototype methods. To add static methods to your class use
extend
. If you want to add
more properties to the prototype of the class later on, use
proto
.
var Module = Stapes.subclass({
constructor : function(name) {
this.name = name;
},
getName : function() {
return this.name;
}
});
var module = new Module('emmylou');
module.getName(); // 'emmylou'
When calling subclass
on a Stapes class you can extend
it into a new class that will inherit all prototype properties of the
parent class.
var Module = Stapes.subclass({
sayName : function() {
console.log('i say my name!');
}
});
var BetterModule = Module.subclass({
sayNameBetter : function() {
this.sayName(); // Inherits 'sayName' from 'Module'
console.log('i say my name better!');
}
});
var module = new BetterModule();
module.sayNameBetter(); // 'i say my name! i say my name better!'
Note that it's perfectly valid to call subclass
without
any arguments at all. In that case you'll simply get a new class
with an empty constructor.
Also note that if you call subclass
on a Module the child
module won't automatically inherit the constructor
of the parent. This is by design. To inherit the constructor of a parent
class simply specify it in your subclass
setup:
var Parent = Stapes.subclass({
constructor : function(name) {
this.name = name;
}
});
var Child = Parent.subclass({
// inherit the constructor from parent
constructor : Parent.prototype.constructor
});
Because subclass
set ups the prototype chain correctly
the instanceof
parameter will work as expected.
module instanceof BetterModule; // true
module instanceof Module; // true
All modules automatically get a parent
property that links
back to the prototype of the parent. You can use this to override a
method in a new class, but still call the method of the parent class, like
the super
method that is available in lots of languages.
Unfortunately super
is a reserved keyword in Javascript, so that's
not usable in Stapes.
var BetterModule = Module.subclass({
// Note that this method name is the same as the one in Module
sayName : function() {
BetterModule.parent.sayName.apply(this, arguments);
console.log('i say my name better');
}
});
var module = new BetterModule();
module.sayName(); // 'i say my name! i say my name better!'
The optional classOnly
flag can be set to true to make
a class without any event or
data methods. You will get all of the
creation methods, so you can still subclass
and extend your class. Use this flag to use Stapes as a simple
class creation library.
var Class = Stapes.subclass({
constructor : function(name) {
this.name = name;
}
}, true /* <-- 'classOnly' flag */);
'subclass' in Class; // true
'get' in Class; // false
extend
module.extend( object[, object...])
Stapes.extend( object )
Extend your class instance properties by giving an
object. Keys with the same value will be overwritten. this
will be set to the objects context.
Module.extend({
"names" : ['claire', 'alice']
"sayName" : function(i) {
console.log( "Hello " + this.names[i] + "!" );
}
});
var module = new Module();
module.sayName(1); // 'alice'
Note that using extend
is exactly the same as directly
assigning properties to the module:
Module.names = ['claire', 'alice'];
// Is the same as
Module.extend({
names : ['claire', 'alice'];
});
Both extend
and proto
accept
multiple objects as arguments:
var module = new (Stapes.subclass());
var instruments = { guitar : true };
var voices = { singing : true };
module.extend(instruments, voices);
console.log('guitar' in module, 'singing' in module); // true, true
extend
is also useful for stuff like configuration
properties.
var Module = new Stapes.subclass({
constructor : function(props) {
this.extend( props );
},
sayInfo : function() {
console.log(this.name + ' plays ' + this.instrument);
}
});
var module = new Module({
'name' : 'Johnny',
'instrument' : 'guitar'
});
module.sayInfo();
Stapes.extend()
can be used for writing extra methods
and properties that will be available on all Stapes modules,
even after you have created them. This is very useful for
writing plugins for functionality that isn't in Stapes.
Stapes.extend({
// Sets an DOM element for views
"setElement" : function(el) {
this.el = el;
this.$el = $(el); // jQuery or Zepto reference
}
});
var Module = Stapes.subclass();
var module = new Module();
module.setElement( document.getElementById("app") );
console.log( module.el ); // "#app" DOM element
console.log( module.$el ); // jQuery or Zepto element
All internal methods are available as the
Stapes._
object, so if you want you can overwrite
and hack virtually all Stapes behaviour. Note that these
methods aren't documented, so you should take a look at the
source.
proto
Module.proto( object )
Adds properties and methods to the prototype of the module.
Note that it's usally easier to directly add methods to the prototype
using the subclass
method.
However,if you want to add methods to the prototype later on,
proto
might be useful.
var Module = Stapes.subclass();
Module.proto({
'sayName' : function() {
console.log('I say my name');
}
});
'sayName' in Module; // false, not a static method
'sayName' in Module.prototype; // true
// Note that using proto is the same as:
Module.prototype.sayName = function() {
console.log('I say my name');
};
Both proto
and extend
accept
multiple objects as arguments. This can be very handy for mixins.
var Module = Stapes.subclass();
var instruments = { guitar : true };
var voices = { singing : true };
Module.proto(instruments, voices);
var module = new Module();
console.log(module.guitar, module.singing); // true, true
API: Events
on
module.on(eventName, handler [, context] )
module.on(object [, context] )
Stapes.on(object [, context] )
Stapes.on(eventName, handler [, context] )
Add an event listener to a Stapes module or object
with mixed-in events. When an event is
triggered the handler
will be called
with two arguments: data
, which may contain any data, and an
eventObject
that contains some useful information about the
event, such as the scope, target and event name.
As an optional third (when defining a single listener) or second
(when defining multipe listeners using an object) parameter you can set what the value of
this
should be in the scope of the event handler.
This is handy to prevent having to temporarily save the scope
to a self
or that
variable or use the
new bind
property of EcmaScript 5.
var Module = Stapes.subclass();
var module = new Module();
module.on('ready', function() {
console.log('your module is ready!');
});
module.on({
"talk" : function() {
console.log('your module is talking!');
},
"walk" : function() {
console.log('your module is walking!');
},
"eat" : function( food ) {
console.log('your module is eating ' + (this.get('food') || 'nothing'));
}
});
var feedme = new Module();
// Set the scope for the event handler to 'module'
feedme.on({
"feed" : function( food ) {
this.set('food', food);
}
}, module);
module.emit('eat');
// "your module is eating nothing"
feedme.emit('feed', 'cookies');
module.emit('eat');
// "your module is eating cookies"
module.get('food');
// "cookies"
feedme.get('food');
// null
The on
method on the global Stapes
object can be used to listen to events from all defined modules.
Listening to the special all
event on the Stapes
global will trigger on all events thrown in all
objects. Very useful for debugging, but be careful not to leave it in
your production code :)
var Module = Stapes.subclass({
constructor : function(name) {
this.name = name;
},
beReady : function() {
this.emit('ready');
}
});
var module1 = new Module('module1');
var module2 = new Module('module2');
Stapes.on('ready', function(data, e) {
console.log('a ready event was triggered in: ' + e.scope.name);
});
module1.beReady(); // 'a ready event was triggered in module 1';
module2.beReady(); // 'a ready event was triggered in module 2';
The all
event listener is also available on every module, so
you can listen to all events from a specific module.
var Module = Stapes.subclass({
"go" : function() {
this.emit('foo');
this.emit('bar');
}
});
var module = new Module();
module.on("all", function(data, e) {
console.log(e.type);
});
module.go(); // first 'foo', then 'bar'
off
module.off(eventType, handler)
module.off(eventType)
module.off()
Removes event handlers from an object. Giving both an eventType
and a handler will remove that specific handler from a module.
Giving only an eventType will remove all handlers bound to
that event type.
With no arguments at all, off()
will remove all event handlers from a module.
var Module = Stapes.subclass();
var module = new Module();
var handler = function(){};
module.on({
"foo" : handler,
"bar" : function(){}
});
module.off("foo", handler); // Removes only the specific handler for foo
module.off("bar"); // Removes all 'bar' handlers
module.off(); // Removes all handlers
emit
module.emit(eventName[, data])
Trigger an event on the module. eventName
can be a space seperated
string if you want to trigger more events. data
can be any
Javascript variable you want, and will be passed to any event listeners
var Module = Stapes.subclass({
"sleep" : function() {
this.emit('sleeping', 'very deep');
}
});
var module = new Module();
module.on('sleeping', function(how) {
console.log("i'm sleeping " + how);
});
module.sleep(); // "i'm sleeping very deep"
mixinEvents
Stapes.mixinEvents([object])
It's possible to add Stapes' event handling
methods to any Javascript object or function. This can be very
handy if you want to create an object that only uses event handlers, or
for an object or function that already exists and you don't want
to convert to a Stapes module.
Here's how to add event methods to an object:
var module = {};
Stapes.mixinEvents(module);
module.on('sing', function() {
console.log("i'm singing!");
});
module.sing = function() {
this.emit('sing');
}
module.sing(); // i'm singing!
Stapes.mixinEvents
returns the object
, so
you could write the first two lines from the previous example even shorter:
var module = Stapes.mixinEvents( {} );
No, wait! It can be even shorter! Without any arguments Stapes.mixinEvents
returns a new object with mixed-in events.
var module = Stapes.mixinEvents();
You can also add event methods to a function:
function Module(what) {
this.what = what;
Stapes.mixinEvents(this);
}
Module.prototype.sing = function() {
this.emit('sing', this.what);
}
var m = new Module("Happy Birthday");
m.on('sing', function(what) {
console.log("i'm singing " + what + "!");
});
m.sing(); // i'm singing Happy Birthday!
Note that these events are also triggered on the main Stapes
object, so you can use Stapes.on
to catch events
from these mixed-in objects as well.
Stapes.on('sing', function(data, e) {
console.log("Singing from " + e.scope.name);
});
var module = Stapes.mixinEvents( {} );
module.name = "a cool module!";
module.sing = function() {
this.emit('sing');
}
module.sing(); // 'Singing from a cool module!'
API: Data methods
each
module.each( function, [context] );
Iterate over all attributes of a module.
When giving a context
parameter this will be set as
the this
value in the iterator function. If context
is not set it will be set to the module itself.
var Module = Stapes.subclass();
var singers = ['Johnny', 'Emmylou', 'Gram', 'June'];
var module = new Module();
module.msg = "I'll be your ";
module.push(singers);
module.each(function(singer) {
console.log(this.msg + singer);
});
// Using the second context parameter of each()
module.singers = new (Stapes.subclass());
module.singers.push( singers );
module.singers.each(function(singer) {
console.log(this.msg + singer);
}, module);
filter
module.filter( function );
Gets an array of attribute values using a custom function.
The callback function
gets two arguments: the value of the attribute, and the original key.
module.push([
{
name : 'Johnny',
playing : false
},
{
name : 'Emmylou',
playing : true
}
]);
var playing = module.filter(function(singer) {
return singer.playing;
}); // [ { name : 'Emmylou', playing : true }]
get
module.get( key );
module.get( key1, key2, ... );
module.get( function );
Gets an attribute by key. If the item is not available will return
null
var Module = Stapes.subclass();
var module = new Module();
module.set({
'instrument': 'guitar',
'name': 'Johnny'
});
module.get('instrument'); // 'guitar'
You can get multiple key / value pairs when you
use more than one argument:
module.get('instrument', 'name'); // { 'instrument' : 'guitar', 'name' : 'Johnny' }
You can also use a function to get a specific value. This is
comparable to filter
,
however, filter
always returns an array of results,
while get
always returns a single result.
getAll
module.getAll();
Returns all the attributes of an module as an object. Handy for JSON
serializing and persistence layers.
Note that this method returns a copy/clone instead of a reference.
getAllAsArray
module.getAllAsArray();
Returns all attributes as an array, so you can easily iterate.
Note that the original key of the attribute is always available as a
'id' key in the the value, provided your value is an object.
Note that this method returns a copy/clone instead of a reference.
module.set({
"name" : "Johnny",
"instrument" : "guitar"
});
module.getAllAsArray().length; // '2'
has
module.has( key );
Checks if a key is available and returns true or false.
module.set('singer', 'Johnny');
module.has('singer'); // true
module.has('instrument'); // false
map
module.map( function, [context] )
Just like each
, map
iterates over
all attributes of a module. map
returns a new array, where every attribute
value of a module has been passed through function
.
module.push([1, 2, 3]);
var arr = module.map(function(nr) {
return nr * 2;
});
console.log(arr); // '[2, 4, 6]'
By default map
gets the module as the value of this
, but this
can be overwritten with the second argument.
push
module.push( value, [silent] );
module.push( array, [silent] );
Sets a value, automatically generates an unique uuid as a key.
You can also push an array of values.
Just as with set
the optional silent
flag will
prevent any change events from being emitted.
For the rest of the behaviour of this method see
set
.
m.push("foo");
m.getAll(); // will look something like { "5323be61-afb8-4034-b408-51132756cd43" : "foo"}
m.push([
"foo",
"bar",
"baz"
]);
push
returns the module, so this method is chainable.
remove
module.remove( key, [silent] );
module.remove( function );
module.remove();
Deletes an attribute. Triggers remove
and
change
events.
remove
also triggers namespaced change
and
remove
events (e.g. change:foo
and
remove:foo
).
You can either use a key
as an argument or a
function
module.remove(function(item) {
return item.done === true;
});
It's possible to remove multiple keys in one go, simply space seperate them:
module.remove('singer instrument johnny');
If you do not want your remove
to trigger an event set
the optional silent
flag to true.
module.remove('singer', true /* <-- silent flag */);
Without any arguments, remove
deletes all attributes in a module and triggers change
and remove
events.
module.push([1,2,3]);
module.size(); // 3
module.remove();
module.size(); // 0
remove
returns the module, so this method is chainable.
set
module.set(key, value, [silent]);
module.set(object, [silent]);
Sets an attribute. Use push
if you want to 'push' a value
with a random uuid, for collections.
To set multiple attributes in one go, use an object as an first argument.
Every attribute will trigger a change
event. A key
that doesn't exist will trigger a create
event, a key
that does exist will trigger an update
event.
All events will have the key of the attribute as their event value.
Special namespaced events will also be triggered. These events have a value
of eventType:key
. So for example, a set
on
an attribute called 'name' will generate a change:name
event. These events will have the attribute value instead of the
key as a data argument in the event callback.
module.on({
"change" : function(key) {
console.log('Something happened with ' + key);
},
"change:name" : function(value) {
console.log('name was changed to ' + value);
},
"create" : function(key) {
console.log("New attribute " + key + " added!");
},
"update" : function(key) {
console.log("Attribute " + key + " was updated!");
}
});
module.set('name', 'Elvis'); // will trigger 'change' and 'create' events
module.set('name', 'Johnny'); // will trigger 'change' and 'update' events
module.set({
"name" : "Elvis",
"instrument" : "guitar"
});
If you do not want your set
to trigger any events set
the optional silent
flag to true
module.set('singer', 'Johnny', true /* <-- silent flag */);
This also works for objects:
module.set({
'singer' : 'Johnny',
'instrument' : 'guitar'
}, true /* silent */);
To get the old or previous value of an attribute
use the mutate
event instead of change
.
There are both namespaced and general versions of this event, just like
change
. Instead of the value of the attribute it
will return an object with oldValue
and newValue
properties. For convenience it also returns the key
of the attribute.
module.set('name', 'Johnny');
module.on({
"mutate:name" : function(values) {
console.log(values.oldValue, values.newValue); // "Johnny, Emmylou"
},
"mutate" : function(values) {
// Returns 'Emmylou'
// Note that this is identical to writing:
// module.on(
// 'change',
// function(key) {
// console.log( module.get(key) );
// }
// );
console.log(values.newValue);
}
});
module.set('name', 'Emmylou');
Note that it's still perfectly fine to assign properties to the
Stapes module directly, as long as you don't overwrite existing
properties. All the data methods are useful if you want to do
model-like stuff, but for ordinary properties that don't need
change events setting attributes using get
and
set
is fine.
module.on('change:name', function() {
// Obviously, this event hander will never trigger
});
module.name = "Elvis";
console.log(module.name); // "Elvis"
set
returns the module, so this method is chainable
Stapes doesn't have a native way of doing validation, but you could overwrite the set
(and possibly update
) method to accomplish the same:
var Person = Stapes.subclass({
set : function(key, value) {
if (key === 'email') {
if (value.indexOf("@") === -1) {
this.emit('error', 'Invalid email adress');
} else {
Stapes.prototype.set.apply(this, arguments);
}
} else {
// Normal set() behavior
Stapes.prototype.set.apply(this, arguments);
}
}
});
var johnny = new Person();
johnny.on('error', function(msg) {
alert( msg ); // 'Invalid email adress'
});
johnny.set('email', 'invalid#email.com');
size
module.size();
Returns the number of attributes in a module.
module.push(['Johnny', 'Emmylou', 'June', 'Gram']);
console.log( module.size() ); // '4'
update
module.update( key, fn, [silent] );
module.update( fn );
Updates an attribute with a new value, based on the return value
of a function.
Just as with set
update
will generate change
and update
events.
module.set('singer', 'Elvis');
module.update('singer', function(singer) {
return 'Johnny';
});
console.log( module.get('singer') ); // 'Johnny';
You can also pass a single function as an argument. In that case,
update
will run on all attributes in the module.
module.push([
{ "name" : "Johnny", "singer" : false},
{ "name" : "Emmylou", "singer" : false}
]);
module.update(function(item) {
item.singer = true;
return item;
});
The callback function in update
gets two arguments: the
value being modified, and the original key. The this
value of the callback will be set to the module you're updating.
The silent
flag will prevent any change events from firing.
update
returns the module, so this method is chainable.
Removed and deprecated stuff
Introduction
These methods, modules and other things are either deprecated
or have been removed. Don't use these features in new code,
and remove any dependencies on them in your current code, in a future
version they might be removed completely.
create (removed)
Stapes.create()
module.create()
Create a new instance of a Stapes object.
This method has been deprecated since 0.7.0 and was completely removed in 0.8.0. Read this blogpost why.
Stapes.util (removed)
Until version 0.5.1 Stapes included a util module with Underscore-like
utilities such as each
and map
. This was
removed in version 0.6.
If your code depends on the Stapes.util
module you can use a compatibility plugin.
Miscellaneous
version
Stapes.version
Returns the current version of Stapes. Note that this property
is only available on the Stapes global variable, not on
individual modules.
Bugs and known limitations
Attributes are stored in an object internally. According to the Javascript spec
objects don't guarantee that properties are returned in order. However, all browsers
do return object properties in order except for Chrome
where numbered keys won't return in order.
In the future this will be fixed, but it requires a big rewrite. For now the best way to
prevent this problem is to simply avoid using numbered attributes. So don't write something like
module.set('1', 'one');
History
- 0.8.1
- Feature
get
now accepts multiple arguments so you can use it like Underscore's pick
(Issue #38). Thanks for the suggestion Santervo!
- Feature
mutate
events are now emitted whenever an attribute is removed (issue #35). Thanks Jasper!
- 0.8.0 - July 9th 2013
create()
has been completely removed after the deprecation in 0.7.0
- Feature
set
now also accepts the silent
flag for objects (issue #28). Thanks for the suggestion Neogavin!
- Feature
remove
without any arguments now removes all attributes in a module.
- Bugfix The
silent
flag did not work with push
(issue #39). Thanks for reporting Gamadril!
- 0.7.1 - February 27th 2013
- Thanks to josher19 the docs now have nice tooltips
for all the methods in the in-code examples!
- Bugfix
Stapes.extend
was broken (issue #33). Thanks gonchuku!
- Bugfix Fixed the todos examples, thanks Erik!
- Bugfix Fixed events in subclasses. (issue #29),
thanks Eric!
- Bugfix Fixed a problem where unbinding an event would throw an error in some rare cases
(issue #30). Thanks Jasper!
- 0.7.0 - January 14th 2013
- Feature Completely revised the creation of new modules with
subclass
. The old create
is still available for backwards compatibility. Read here why i deprecated create
.
- Feature Added a
map
function to every module.
- Feature
update
now gets the module set as the
this
context, and gets the key in the callback function.
- Feature
update
now has a silent
option too.
- Feature
remove
now accepts multiple keys to remove.
- Bugfix
getAllAsArray
no longer overwrites
an id
value if its present in the object
- 0.6 - October 14th 2012
- Feature
remove
now also triggers namespaced events
(issue #13).
- Feature
set
, push
and
remove
now have an optional silent
flag that
will preveny any events from being triggered (issue #18)
- Feature
push
, set
,
remove
and update
now return the
module, so you can chain these methods (issue #17)
- Bugfix Specific events that were emitted on
Stapes.on
gave a wrong scope (issue #19)
- Bugfix Events didn't bubble up to the global
Stapes
object
(issue #12)
- Bugfix Fix for the
remove
handler in IE8. Thanks @wellcaffeinated!
Stapes.util
has been removed. If your code depends on it you can use a compatibility plugin.
- 0.5.1 - July 20th 2012
- Feature All private methods are now part of the
Stapes._
which means
plugin authors can overwrite and redefine every part of Stapes.
- Bugfix Fixed a bug where calling create() on a module wouldn't increase the guid
(issue #8). Thanks
@wellcaffeinated!
- 0.5 - July 2nd 2012
- Feature Add event to any method using the
mixinEvents
method
- Feature Added the
off
event method to remove event handlers
- The two todos examples are updated to the latest version from
TodoMVC
- 0.4 - May 10th 2012
- Feature Added the whole bunch of utility methods.
- Feature Added an
each
method to Modules for easy iteration over attributes
- Feature Added a
size
method to get the number of attributes in a module.
- Bugfix Data in event handlers was silently changed to
null
if it was falsy,
so passing false
as a data argument would result in handlers getting null
instead of
the expected data argument.
- Updated the two todos examples, using the versions from the TodoMVC collection
- Removed the undocumented
init
method that was part of every Stapes module
- Rewrote the util functions for cleaner code (including a
map
and an each
with a context parameter).
- 0.3 - April 5th 2012
- Feature Added the
mutate
change event.
- Feature
update
now accepts a single function as an argument too.
- Bugfix Setting an attribute with the same value as the old value doesn't trigger a change event anymore.
getAll()
and getAllAsArray()
now return a clone of the attributes instead of a reference.
- Removing the undocumented
changemany
and createmany
events.
- 0.2.1 - March 28th 2012
- Fixed a bug where global events didn't always work
because the guid was set to 0 initially. Thanks
@frenkie!
- 0.2 - March 4th 2012
Contributors
Thanks to all of you for contributing code, docs, reporting bugs, giving good advice and inspiration!


Numpy tricks: Element-wise multplication of rows of two matrices
While working on a project I came across a situation where I had to do an element-wise multiplication of rows of two matrices to produce a 3rd-order tensor. A few minutes of Googling did not give me an efficient solution. So here is a solution that is faster than the naive approach of using python list comprehension.
Problem
Let \(\mathbf{A}\) be a \(m \times n\) matrix and \(\mathbf{B}\) be a \(p \times n\) matrix. We want a \(m \times p \times n\) tensor \(\mathbf{C}\) such that \(\mathbf{C}_{i,j} = \mathbf{A}_{i} \circ \mathbf{B}_{j}\), where \(\mathbf{A}_i\) is the i-th row of A and \(\mathbf{B}_j\) is the j-th row of B.
Solution
Assume we have the following matrices:
Naive solution
The following uses python list comprehension:
Solution using einsum
The following uses Einstein notation function einsum of numpy:
Performance
Not only is the einsum approach much shorter, it is also about 10 times faster than the naive approach. Here are some quick benchmark results on my system running OS X.
In the first approach creating a new array and reshaping it are additional operations that the einsum method doesn’t have. So to get an idea about the time it takes to just multiply the rows using python list comprehension I ran the following benchmark:
From the above it is clear that the bulk of the time is spent in looping, which is slow, rather than creating a numpy array and reshaping it.
Concluding remarks
The einsum function in numpy is a powerful construct that can be used to represent complex matrix operations in a compact way and can result in significant performance improvement over loops. It is worth learning the Einstein sum notation, even for it’s own sake — it is pretty cool after all.


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This game mode is for decreasing the time alotted to every set of questions by a specific percentage. You can select the percentage from the below option to reduce the time per question by the selected percentage.


The Drop Down Llama Menu II full description can be found in the corresponding post.
© Seamus P. H. Leahy You may take and improve upon this. Updated: 2006.9.24


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syndaemon
Section: User Commands (1)Updated: xf86-input-synaptics 1.4.1
Index Return to Main Contents
NAME
syndaemon - a program that monitors keyboard activity and disables the touchpad when the keyboard is being used.
SYNOPSIS
syndaemon [-i idle-time] [-d] [-p pid-file] [-t] [-k] [-K] [-R] [-s]
DESCRIPTION
Disabling the touchpad while typing avoids unwanted movements of the pointer that could lead to giving focus to the wrong window.
OPTIONS
- -i <idle-time>
- How many seconds to wait after the last key press before enabling the touchpad. (default is 2.0s).
- -d
- Start as a daemon, ie in the background.
- -p <pid-file>
- Create a pid file with the specified filename. A pid file will only be created if the program is started in daemon mode.
- -t
- Only disable tapping and scrolling, not mouse movements, in response to keyboard activity.
- -k
- Ignore modifier keys when monitoring keyboard activity.
- -K
- Like -k but also ignore Modifier+Key combos.
- -R
- Use the XRecord extension for detecting keyboard activity instead of polling the keyboard state.
- -s
- Use a shared memory area to enable/disable the touchpad instead of device properties. WARNING: The SHM mechanism is not secure if you are in an untrusted multiuser environment. All local users can change the parameters at any time. This option requires the driver Option "SHMConfig" to be enabled.
ENVIRONMENT VARIABLES
- DISPLAY
- Specifies the X server to contact.
CAVEATS
It doesn't make much sense to connect to a remote X server, because the daemon will then monitor the remote server for keyboard activity, but will disable the touchpad on the local machine.
AUTHORS
Peter Osterlund<EMAIL_ADDRESS>- This man page was written by Mattia Dongili<EMAIL_ADDRESS>SEE ALSO
Xorg(1), synclient(1), synaptics(4)
Index
This document was created by man2html, using the manual pages.
Time: 05:29:11 GMT, December 24, 2015


chromap - fast alignment and preprocessing of chromatin profiles
* Indexing the reference genome:
chromap -i [-k kmer] [-w miniWinSize] -r ref.fa -o ref.index
* Mapping (sc)ATAC-seq reads:
chromap --preset atac -r ref.fa -x ref.index -1 read1.fq -2 read2.fq -o aln.bed [-b barcode.fq.gz] [--barcode-whitelist whitelist.txt]
* Mapping ChIP-seq reads:
chromap --preset chip -r ref.fa -x ref.index -1 read1.fq -2 read2.fq -o aln.bed
* Mapping Hi-C reads:
chromap --preset
hic -r ref.fa -x
ref.index -1 read1.fq -2
read2.fq -o aln.pairs
chromap --preset hic -r ref.fa
-x ref.index -1 read1.fq
-2 read2.fq --SAM -o aln.sam
Chromap is an ultrafast method for aligning and preprocessing high throughput chromatin profiles. Typical use cases include: (1) trimming sequencing adapters, mapping bulk ATAC-seq or ChIP-seq genomic reads to the human genome and removing duplicates; (2) trimming sequencing adapters, mapping single cell ATAC-seq genomic reads to the human genome, correcting barcodes, removing duplicates and performing Tn5 shift; (3) split alignment of Hi-C reads against a reference genome. In all these three cases, Chromap is 10-20 times faster while being accurate.
Indexing options
|
-k INT |
Minimizer k-mer length [17]. | ||
|
-w INT |
Minimizer window size [7]. A minimizer is the smallest k-mer in a window of w consecutive k-mers. |
--min-frag-length
Min fragment length for choosing k and w automatically [30]. Users can increase this value when the min length of the fragments of interest is long, which can increase the mapping speed. Note that the default value 30 is the min fragment length that chromap can map.
Mapping
options
--split-alignment
Allow split alignments. This option should be set only when mapping Hi-C reads.
|
-e INT |
Max edit distance allowed to map a read [8]. | ||
|
-s INT |
Min number of minimizers required to map a read [2]. |
-f INT1[,INT2]
Ignore minimizers occuring more than INT1 [500] times. INT2 [1000] is the threshold for a second round of seeding.
|
-l INT |
Max insert size, only for paired-end read mapping [1000]. | ||
|
-q INT |
Min MAPQ in range [0, 60] for mappings to be output [30]. |
--min-read-length INT
Skip mapping the reads of length less than INT [30]. Note that this is different from the index option --min-frag-length , which set -k and -w for indexing the genome.
--trim-adapters
Try to trim adapters on 3’. This only works for paired-end reads. When the fragment length indicated by the read pair is less than the length of the reads, the two mates are overlapped with each other. Then the regions outside the overlap are regarded as adapters and trimmed.
--remove-pcr-duplicates
Remove PCR duplicates.
--remove-pcr-duplicates-at-bulk-level
Remove PCR duplicates at bulk level for single cell data.
--remove-pcr-duplicates-at-cell-level
Remove PCR duplicates at cell level for single cell data.
--Tn5-shift
Perform Tn5 shift. When this option is turned on, the forward mapping start positions are increased by 4bp and the reverse mapping end positions are decreased by 5bp. Note that this works only when --SAM is NOT set.
|
--low-mem |
Use low memory mode. When this option is set, multiple temporary intermediate mapping files might be generated on disk and they are merged at the end of processing to reduce memory usage. When this is NOT set, all the mapping results are kept in the memory before they are saved on disk, which works more efficiently for datasets that are not too large. |
--bc-error-threshold INT
Max Hamming distance allowed to correct a barcode [1]. Note that the max supported threshold is 2.
--bc-probability-threshold FLT
Min probability to correct a barcode [0.9]. When there are multiple whitelisted barcodes with the same Hamming distance to the barcode to correct, chromap will process the base quality of the mismatched bases, and compute a probability that the correction is right.
|
-t INT |
The number of threads for mapping [1]. |
Input options
|
-r FILE |
Reference file. | ||
|
-x FILE |
Index file. | ||
|
-1 FILE |
Single-end read files or paired-end read files 1. Chromap supports mulitple input files concatenate by ",". For example, setting this option to "read11.fq,read12.fq,read13.fq" will make all three files as input and map them in this order. Similarly, -2 and -b also support multiple input files. And the ordering of the input files for all the three options should match. | ||
|
-2 FILE |
Paired-end read files 2. | ||
|
-b FILE |
Cell barcode files. |
--barcode-whitelist FILE
Cell barcode whitelist file. This is supposed to be a txt file where each line is a whitelisted barcode.
--read-format STR
Format for read files and barcode files ["r1:0:-1,bc:0:-1"] as 10x Genomics single-end format.
Output options
|
-o FILE |
Output file. |
--output-mappings-not-in-whitelist
Output mappings with barcode not in the whitelist.
--chr-order FILE
Customized chromsome order.
|
--BED |
Output mappings in BED/BEDPE format. Note that only one of the formats should be set. |
--TagAlign
Output mappings in TagAlign/PairedTagAlign format.
|
--SAM |
Output mappings in SAM format. | ||
|
--pairs |
Output mappings in pairs format (defined by 4DN for HiC data). |
--pairs-natural-chr-order FILE
Natural chromosome order for pairs flipping.
|
-v |
Print version number to stdout. |
Preset
options
--preset STR
Preset []. This option applies multiple options at the same time. It should be applied before other options because options applied later will overwrite the values set by --preset. Available STR are:
|
chip |
Mapping ChIP-seq reads (-l 2000 --remove-pcr-duplicates --low-mem --BED). | ||
|
atac |
Mapping ATAC-seq/scATAC-seq reads (-l 2000 --remove-pcr-duplicates --low-mem --trim-adapters --Tn5-shift --remove-pcr-duplicates-at-cell-level --BED). | ||
|
hic |
Mapping Hi-C reads (-e 4 -q 1 --low-mem --split-alignment --pairs). |


X-Puzzle
The X-Puzzle is a great way to inform and entertain customers and prospects in a fun way. The number of pieces can be personalised to your requirements. Each piece can be mailed to customers and prospects supporting a frequent, entertaining and helpful contact. Enable your customers to remember your brand with something fun, personal and unique.
For more information contact Simran Gill on 01753 215333 or email<EMAIL_ADDRESS>. . . . . . . . . .

X-Puzzle supports our main business objective – helping our customers maximise their investment when they buy from us.


{% extends "_base.html" %} {% block social_title %}{% block title %} About — EU Trials Tracker {% endblock %}{% endblock %} {% block social_description %} By EU law, from December 2016, all trials on the European Union Clinical Trials Register (EUCTR) must post results within 12 months of completion. This is the first legislation enacted anywhere in the world which requires such trial publication. EU Trials Tracker shows which organisations are compliant and which aren't. {% endblock %} {% block content %}
Non-reporting of clinical trial results is an ongoing global public health problem.
The best currently available evidence shows that around half of all trials go unreported: this means that doctors and patients see only a partial, biased fraction of the true evidence. We cannot make informed decisions about treatments unless all the data is reported. Under EU rules, from December 2016, all trials on the European Union Clinical Trials Register (EUCTR) should post results within 12 months of completion. There has never been a rule as simple and clear as this, anywhere in the world. Our EU Trials Tracker shows which organisations are compliant, and which aren't. Our paper in the BMJ analysed the data as of January 2018, and found that only 49% of Europe's clinical trials reported results in the register.
This website is one of a series of Trials Trackers produced by the Bennett Institute for Applied Data Science at the University of Oxford.
Clinical trials are the gold standard in medicine: they are the most fair test of whether a treatment really works; they are also used to assess how one treatment compares to other available options. In a clinical trial, the treatment is usually given to real patients, in a real-world setting. The outcomes measured are ideally real-world problems that matter to patients, such as pain, disability or death; but can also include lab tests, or scans.
We use the results of clinical trials to make real-world decisions about which treatments work best. We can’t make informed choices if the results of clinical trials are withheld from doctors, researchers, and patients. Read more about this from the AllTrials Campaign.
Yes! You can read our full paper including further statistical analyses, technical details regarding our methods, and a longer discussion of the background and implications of this work in The BMJ
Citation:Goldacre B, DeVito NJ, Heneghan C, et al. Compliance with requirement to report results on the EU Clinical Trials Register: cohort study and web resource. BMJ 2018;362:k3218.
The Bennett Institute for Applied Data Science at the University of Oxford: we are a truly multi-disciplinary team of clinicians, academics, and software engineers working together to make data more impactful in the real world. Francis Irving and Seb Bacon were the software engineers for the site; Ben Goldacre was the principal investigator; Nick DeVito was the researcher; with contributions from the Bennett Institute team and Open Knowledge International.
Email us<EMAIL_ADDRESS>We'd particularly like to hear about any errors, omissions or ideas.
This data updates regularly, on a monthly cycle. We think it’s important that information about who is reporting clinical trials is current and regularly updated: so that sponsors are always motivated to improve; and sponsors who do improve can see their good work reflected in public. The current data was taken from the register starting on {{ scrape_date }}. All clinical trials on medicinal products (drugs and vaccines) conducted in Europe since 2004 are in the register. For full details, see the register's about page.
When more than a year has passed since the completion of a trial, the results should be published, and we call it "due". Specifically, we take the latest “global end of trial date” listed for the trial; then add a year (the maximum delay permitted for sponsors to report results); and finally add 4 weeks (the statutory maximum 15 days administrative delay for results to be published on the register by the regulator, and another 5 days to allow for national holidays and exceptional circumstances). Currently, any trial completed earlier than {{ due_date_cutoff }} is due. You can read a detailed description of the way we assess an individual trial here
The initial table on the front page shows only sponsors with 50 or more total trials in the register. This is to make the headline rankings more easily viewable. If you click “all sponsors” you can see all sponsors! This is a list of thousands, so we have also made a search box where you can find a sponsor you are particularly interested in.
“Inconsistent Data” means that we cannot definitively say the trial is due to report with the data provided on the EUCTR. This could be for any number of reasons involving the sponsor (for not providing timely and accurate information), national competent authorities (for failing to quality control submissions or update entries), and/or the design and implementation of the EUCTR itself:
Currently, we identify the following issues:
While we cannot accurately assess the status of these trials, they may still have results. We note this in the label next to the trials. When the fault lies with the sponsor, we think the EU registry managers could and should automatically identify trials with inconsistent data, as we have done; and then require sponsors to correct their records.
We have included a tag to identify when trials are “Terminated” for all locations (called “Prematurely Ended” on EUCTR). A trial that ends early, but enrolled and collected data on patients, is required to report results under EU Guidelines. In some instances trials are registered on the EUCTR but are withdrawn before starting enrollment, and therefore have no data to report. The EUCTR has no reliable way to show that a trial never started, however sponsors may be able to use workarounds to ensure these trials show up as properly reported. If the trial ended prior to July 2013, you should have the ability to upload a statement that the trial never began and satisfy the reporting requirement. For trials that ended after July 2013, you may be able to combine a statement with "null" codes for the required areas. An example of this is available here. For more details on this see Jackie Pullen's presentation from the QUEST Clinical Trials Workshop 2019 from the links here. We will continue to evaluate terminated trials as due to report, so as not to miss legitimate trials due to report, and those “Terminated” for all locations will have a tag denoting this. We hope to be able to exempt these trials from the tracking statistics entirely once the EUCTR system is improved to better handle this issue.
Some trials in our “Not Due” category would never become due because they are identified as a Phase 1 trial that is not part of a Paediatric Investigation Plan. These types of trials are not covered by the reporting guideline and are typically not made public on the EUCTR. However, some trials meeting this description are available on the EUCTR. There may be some reason why these trials are made public and required to report, however to remain conservative, we now identify these trials as “Exempt” and they remain in the “Not Due” category.
Over time organisations can merge, change names, or split: companies may acquire other companies; universities may join together; and so on. If we think an organisation is now effectively part of another, we say so at the bottom of its page. Conversely, if an organisation now effectively includes other organisations, and so is responsible for their trials, we list those at the bottom of its page. The trials of the smaller organisations are not included in the counts of the larger one. We've made every effort to get these relationships right; there is no canonical data source on mergers and acquisitions; if you think we should update any of our data on this, please tell us.
Due to Brexit, as of 1 January 2021, new trials from the UK will no longer be registered on the EUCTR. Any UK protocols that were in "Ongoing" status as of the end of 2020 are now locked in the status "GB - no longer in EU/EEA" and can no longer be updated. This means ongoing trials registered exclusively in the UK will never have completion data appear. While sponsors may still upload results, we will not be able to reliably assess the due date of these trials. For trials registered in more than one location that include the UK, we will ignore the UK protocols in status "GB - no longer in EU/EEA" when determining if a trial is complete or not. As of January 2021, this has not yet been implemented but we are working to adjust our code to incorporate these changes as soon as possible. When this is implemented, some "Not Due - Ongoing" trials will move into the "Due" category if the only outstanding uncompleted trial is a UK trial. We expect this will effect a relatively small number of trials and no assessments of currently due trials should be impacted due to Brexit.


Upasana Metals proudly welcomes you to the world where quality and flawless service are prime objectives. This motto has made us the leading trader of industrial grade ferrous and non-ferrous metals.
The company was originated in 2005 in Ahmedabad and right from its inception the company has firmly believed that gender or geographical boundaries do not limit the growth of human progress. Now we are one of the most reliable sources of Industrial grade metals covering the entire Western Region including the coastal areas.
In 2004, we branched out a new company as an executive unit for reformed metal products. This company is dealing with cable trays, wire mesh, perforated sheets etc. of various metals. As the member of Upasana Metals, the company brings synergistic strength & experience of years in the metal trading industry.


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{% extends 'base.html' %} {% block content %}
Browse errors found by DeepOSM, and pop to iD editor on openstreetmap.org to correct.


Before Change
column = y_df[col]
num_hit = 0
num_required = required_hit_dict[colIndex]
for index, value in y_df[col].iteritems():
if pd.notnull(value):
num_hit += 1
// check to see if number of hits has been hit
After Change
def __generate_required_index(self, w, required_hit_list):
colIndex = 0
index_hits = []
//loop through each column and obtain index required to splice out for frac train hits
for col in w.T:
num_hit = 0
num_required = required_hit_list[colIndex]
for index, value in enumerate(col):
if value != 0:
num_hit +=1
if num_hit >= num_required:
index_hits.append(index)
break
colIndex += 1
return index_hits


Home > Festival Origins
A Vision Brought to Life
The Porter Fleming Foundation was created in 1963 by Barry Fleming to honor his father: painter and writer Porter Fleming. The Trustees of the Academy of Richmond County work on behalf of the Porter Fleming Foundation administering grants and fellowships to organizations and individuals who demonstrate excellence in the fields of education, literature, art, science, history, music and culture. In 2005, the Foundation received a bequest from Shirley Fleming's estate. Ms. Fleming, an artist like her father and grandfather, was a highly regarded music critic in New York City until her death in 2005. During her career in New York, she maintained a home in and a passion for Augusta, Georgia. In 2005, the Trustees had a vision of creating a festival that would culturally enrich the Augusta's residents and visitors. There began the planning for the first Westobou Festival. These visionaries first came up with the name, Westobou. The Westobou River, the former name of the Savannah River, was derived from the Westo Indians who migrated to Augusta in the 1660's. The Savanna Indians defeated the Westo Indians in 1680, and the river that now runs through downtown Augusta remains named after the Savanna Indians, the Savannah River.
What is the Westobou Festival?
Westobou Festival puts a spotlight on the Central Savannah River Area through a celebration of national and international talent. The festival prides itself on its ability to connect our audience with everything from award winning premier artistic performances to rock concerts. Westobou maintains a high quality of performances appealing to all.
Celebrating excellence in the arts, the festival includes an array of performances and exhibitions featuring distinct talent in the disciplines of dance, film, music, spoken words and visual arts. Westobou Festival gives audiences the opportunity to experience the power of art within the backdrop of our exciting city.
Where is the Westobou Festival?
The Westobou stage can not be contained within a single venue, but can been seen throughout the Central Savannah River Area: including downtown Augusta, Augusta State University, Paine College and North Augusta, SC.
Westobou festival headquarters is The Old Academy of Richmond County. Chartered in 1783, this historic property plays hosts to visual art exhibitions and concerts. In 2011, the festival presented five concerts on the adjacent Parade field including Roseanne Cash, Blue Rodeo and Sharon Jones and the Dap Kings. The success, and beauty, of the Parade grounds will continue to play a vital role in the festival.


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🧩 DEGO x Mask Network | Build the NFT entrance in Web 3.0
Mask Network has reached a strategic partnership with cross-chain NFT and DeFi protocol DEGO Finance. Both parties will work together in fields such as NFT blind boxes, games, and social networks. Users will be able to conduct NFT creation, collection, buying and selling on Twitter, all with a few clicks.
🔒 Mask Network x Cent | Buy the Tweet you just saw on Twitter
Mask Network is collaborating with Cent through a joint bounty to add NFTs directly to Twitter: bid and trade on tweets directly within Twitter to support those who tweet.
Sample:
Bounty:
https://gitcoin.co/issue/DimensionDev/Maskbook/2599
🔗 Mask Network partners with NEAR Protocol, raising a joint bounty to kick it off
Mask Network reached a strategic partnership with the PoS blockchain NEAR Protocol. The Rainbow Bridge, the NEAR EVM, NEAR Drop, and other key components are expected to be integrated with Mask Network. This cooperation started with a joint bounty: to integrate NEAR Wallet into Mask Network, creating a solid foundation for future partnership.
Bounty:
https://gitcoin.co/issue/DimensionDev/Maskbook/2602/100025151
Mask Network has invested and partnered with decentralized interchangeable asset protocol Convergence. Projects on Convergence could conduct Wrapped Security Token launchings through Initial Twitter Offering and trade them in the Convergence AMM pool.
🙌 Mask Network x Polygon|Other ways to play?
Mask Network has collaborated with Layer 2 solution aggregator Polygon (formerly Matic Network), to conduct technical conversations about the current issues, such as traffic and high gas fee on Ethereum. Mask Network will first integrate QuickSwap, a decentralized exchange that is part of Polygon’s ecosystem through a joint bounty.
Bounty:
https://gitcoin.co/issue/DimensionDev/Maskbook/2645/100025307
🎉 Mask Network x Gitcoin | Gitcoin Grants Round 9
Mask Network has been an active funder since Gitcoin Grants Round 6, and has published more than 20 bounties on Gitcoin. Meanwhile, MaskNetwork keeps on supporting the Gitcoin Grants Round 9, encouraging more developers into the ecosystem building of future blockchain and the development of open-source project.
Mask Network reached a technical partnership with Gitcoin years ago. Mask Network can automatically recognize Gitcoin donation links, so users could donate with a few clicks after the installation of the extension. We also had a MASK Webinar during the GR9, click “HERE” to get the full video of introductions of how to support the Gitcoin Grant directly from Twitter and other cool features we have.
💰 $MASK is now on Transak, supporting direct buying on Twitter
$MASK token is now on Transak, the fiat on-ramp aggregator endorsed by ConsenSys. Users can buy $MASK token directly using fiat without leaving Twitter.
📍Token Unlock Details (March 2021)
It has been about a month since the official launch of the $MASK token, the first $MASK unlock took place on March 29th, 2021 (UTC+8).
Github https://github.com/DimensionDev
Twitter https://twitter.com/realMaskNetwork
Facebook https://www.facebook.com/masknetwork
Discord https://discord.com/invite/cKGW45g
Telegram (English) https://t.me/maskbook_group
Telegram （中文） https://t.me/masknetwork_cn


Wall Street edges higher at open with focus on Trump speech
U.S. stock index futures were largely flat on Tuesday, as investors turned their focus to a speech by President Donald Trump for clarity on U.S.-China trade relations.
REUTERS: U.S. stocks eked out slim gains at open on Tuesday, buoyed by technology stocks, as investors looked forward to a speech by President Donald Trump later in the day for clarity on U.S.-China trade relations.
The Dow Jones Industrial Average rose 10.10 points, or 0.04per cent, at the open to 27,701.59. The S&P 500 opened higher by 2.27 points, or 0.07per cent, at 3,089.28. The Nasdaq Composite gained 6.80 points, or 0.08per cent, to 8,471.07 at the opening bell.
(Reporting by Medha Singh in Bengaluru; Editing by Sriraj Kalluvila)


Copyright 2011 the Authors for http://usdlc.net
use http://github/usdlc/usdlc to confirm author contribution
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
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Unless required by applicable law or agreed to in writing,
software distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.


COVID-Rating is a platform where businesses will be rated by their prevention practices. Consumers rate a restaurant based on its measures to stop the spread of COVID-19. These reviews can be accessed by other health conscious consumers to ultimately help decide on where to eat. Especially as restaurants are reopening, it is imperative that consumers are well educated on the restaurant's preventative practices. COVID-Rating provides other helpful information relating to COVID like providing live traffic reports and parking/walking space situation. COVID-Rating caters to the new preference and demand
Rate a business based on their COVID practices
Are they wearing protectiv gear?
Are they social distancing?
Do they offer social distance seating?
Report any new requirements in order to enter the restaurant
Keep a track of your reviews
Learn about COVID
Take photos and post them to your review
Learn how to properly wear a mask
Find out about Symptoms,
Testing, & Vaccines
Advice for the Public
Travel Advice
Situtation Reports
Social Distancing
Local Restrictions
State-by-State Map of
COVID-19 Guidance
The creators of COVID-Rating


Hello. This page, hosted on Github is the place where I currently put my stuff in it.
Links:
I am not really good at really expressing my ideas and language


It also provides other major information like timings, doctor specialisation, number of beds, OT, hosiptal's contact details and ambulance


REQUEST: Cover-only mode (no text) for floater
Bugzilla not sending emails
Synergy downloads album art even though art already embedded in iTunes
REQUEST: Use hot key to call up iTunes-style search field
REQUEST: Do not display Synergy icon in Floater if no album art available
Synergy uses a lot of memory
REQUEST: Indicate next track when in shuffle mode
REQUEST: Add "relative" domain for installs to non-hard-coded paths
REQUEST: Add executable to "MacOSClassic" folder explaining that Install is for Mac OS X only
REQUEST: Specify files to remove using bundle identifiers, creator codes or partial paths


{% extends "base.html" %} {% block content %} Edit your post Title Content {{content}} {{error}} SUBMIT DELETE OR Cancel
{{error}}
Are you sure you want to delete this post? You will lose it forever!


Select your shipping method above. Please note: regular shipping rates shown are based on the subtotal before discounts are taken and may not reflect special shipping promotions.
Standard Ground should arrive between June 9 and June 15.
Priority Air should arrive between June 7 and June 8.
Alaska/Hawaii - Standard Ground should arrive between June 9 and June 15.
APO/FPO - Standard Ground should arrive between June 9 and June 15.


Miss.d is used to send you alerts when regularly scheduled jobs don't trigger after a certain period of time. Each job you create comes with an API key which your job should POST to after completion. If your job does not POST to Miss.d within the expiration time period your job notifications are sent out.
To force expire a job (e.g. a job is in a known bad state) send a POST to {{expireUrl('your-api-key')}}.


Hi! I'm a software engineer at Microsoft on the Edge Progressive Web Apps team.
I graduated from UT Austin with a B.S. in Computer Science in 2020.
During college, I interned at Amazon for two summers.
I have experience working with C++, Java, C#, Node.js, and Python through work, class, and side projects.
In my free time, I enjoy basketball, learning Japanese, working out, fantasy football, and gaming.
See my resume here. abhinavkasamsetty@gmail.com


JavaScript (JS) is a programming language or, in other words, a way to tell a computer to do things. All web browsers understand JavaScript and you can take advantage of that to make web pages interactive.
JavaScript started as a way to make web pages more interactive by adding movement. Nowadays JavaScript runs in more places than just web browsers — it runs on phones and even robots!
In Lesson 1 you will learn how to create Strings.
In Lesson 2, you will learn how to add values and variables.
In Lesson 3, you will learn about using functions.
Each lesson should take about 20 minutes. Adding samples in DevMode will take a little longer.


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FAITH ACADEMY
French Carnival
Welcome,
We would like to thank you all for your participation in the "Online Celebration of French Carnival".
To access your certificate, please choose your shift from below-